Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances

Abstract

Perturbation of mitochondrial DNA (mtDNA) gene expression can lead to human pathologies. Therefore, a greater appreciation of the basic mechanisms of mitochondrial gene expression is desirable to understand the pathophysiology of associated disorders. Although the purpose of the mitochondrial gene expression machinery is to provide only 13 proteins of the oxidative phosphorylation (OxPhos) system, recent studies have revealed its remarkable and unexpected complexity. We review here the latest breakthroughs in our understanding of the post-transcriptional processes of mitochondrial gene expression, focusing on advances in analyzing the mitochondrial epitranscriptome, the role of mitochondrial RNA granules (MRGs), the benefits of recently obtained structures of the mitochondrial ribosome, and the coordination of mitochondrial and cytosolic translation to orchestrate the biogenesis of OxPhos complexes.

Figure 1

Mitochondrial Gene Maintenance and Expression: A Focus on Post-Transcriptional Processes. Proteins involved in mitochondrial gene maintenance and expression have been localized to focal nucleoprotein structures in the mitochondrial matrix. These foci can be classified according to their protein contents into nucleoids, which contain mitochondrial (mt)DNA and mtRNA granules (MRGs, represented in dark orange). Nucleoids and MRGs are present in close spatial proximity in microscope analyses. Nucleoids contribute mainly to the maintenance of the genetic material of mitochondria and the synthesis of RNA. Characterization of MRGs revealed the presence of a panoply of enzyme classes that perform diverse tasks necessary for the post-transcriptional expression of mitochondrial genes, from RNA maturation to mitoribosome assembly. However, it is currently not clear if all post-transcriptional steps of mitochondrial gene expression occur in MRGs. RNA degradation, the last stage of RNA metabolism, has also been postulated to occur in specialized foci, termed D-foci (shown in light orange), that contain the components of the mitochondrial degradosome, RNA helicase Suv3 and PNPase. A portion of D-foci have been found to colocalize with newly synthesized mtRNA, in a similar manner to MRGs, and may represent a subpopulation of MRGs participating in RNA processing or degradation mediated by the degradosome. Following maturation of all three classes of mtRNAs, mitoribosome assembly, and mt-tRNA aminoacylation, these molecules are now available for utilization in mitochondrial protein synthesis. Mitoribosomes synthesize 13 OxPhos proteins encoded by mt-mRNAs, and these subunits are co-translationally inserted into the inner mitochondrial membrane where they are incorporated into respiratory complexes together with nucleus-encoded OxPhos subunits. The stages of mitochondrial gene expression relevant for this review are indicated in orange.

Figure 2

Known Players in Mammalian Mitochondrial Ribosomal Biogenesis. Following endonucleolytic cleavage of newly transcribed polycistronic mitochondrial RNA (mtRNA) transcripts, mitochondrial ribosomal RNAs (mt-rRNAs) must undergo a series of nucleotide modifications. There are five known modified residues in mammalian 12S mt-rRNA and five in 16S mt-rRNA. The exact residues and their modifications are indicated in brackets and relate to the position in human 12S or 16S mt-rRNA. Shown in blue are the enzyme factors that are known to modify the indicated positions on mt-rRNAs. Several methyltransferases have been identified which modify mt-rRNAs, with NSUN4 and TFB1M modifying 12S and TRMT61B, and MRM1, MRM2, and MRM3 modifying 16S, at the indicated positions. In addition, pseudouridine synthase RPUSD4 has been identified as enzyme that is likely to provide the Psi1397 modification. In addition to nucleotide modifiers, several further protein factors are required for assembly of mitochondrial ribosomal proteins (MRPs) into the mitochondrial large ribosomal subunit (mt-LSU), the mitochondrial ribosomal small subunit (mt-SSU), or to aid in the formation of the complete monosome. These accessory factors are shown in orange. Although the enzymatic role of some of these factors have been predicted or can be inferred from their bacterial homologs, such as the putative RNA helicases MDDX28 and DHX30, or the proposed RNA chaperone ERAL1, the precise roles of many of the indicated accessory factors in mitoribosome biogenesis have yet to be determined. ‘?’ indicates a known nucleotide modification or assembly step where the responsible factors are yet to be identified. Because MRPs have been found to copurify with the mitochondrial nucleoid and mtRNA granules (MRGs), early steps of mitoribosome assembly are likely to occur co-transcriptionally, in concert with mt-rRNA nucleotide modifications. The factors that have, thus far, been found to localize to MRGs are in solid color. Abbreviations: LSU, large subunit; PSI, pseudouridine; SSU, small subunit.